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Friday, December 14, 2012

I am very excited! I am going to attend a conference on communicating Science to the public. The National Evolutionary Synthesis Center (NESCent; http://www.nescent.org), in Durham, North Carolina, has committed financial support and resources for a three-day catalysis meeting devoted to this project.Nothing like a meeting (and deadlines) to motivate me to write more about science.The only problem is that I'm too busy doing science to write about it!! I'd say that there will be a break coming up, but I'm trying to get some analysis done for a collaborator with a grant deadline the first week of February. That means she needs the results by early January... in just a few weeks!!The wonderful thing is that I don't really feel pressure (yet), because the project, and analysis is just so interesting. So with that, back to it!!

Thursday, December 13, 2012

Near the completion of my PhD, I was in the office, turning in some paperwork when one of the administrative assistants got my attention to point out the man leaving the office. His name was J. Lloyd Huck, the person who made the Huck Institutes for Life Sciences, and my degree in Bioinformatics and Genomics, possible.

Being me, I sat down my papers, and awkwardly walked/jogged up to just a few steps behind him then slowed because I didn't have any clue what to say. He was a fast walker, and we'd be to the main street before I knew it, so I took a breath, two large steps and loudly said, "excuse me". I apologized for interrupting him, and clumsily explained who I was, and thanked him for supporting the sciences. I remember it as being pretty ungraceful in my mind, so I can only imagine what he thought of the bumbling grad student in front of him. Still, he was gracious, and polite, and then on his way.

I hope that his family and friends have all of the love and support they need. I have one small memory of him in person, but will have a lifetime knowing that his generosity touched my life, and gave me the opportunity to pursue my life's passion in scientific research.

Wednesday, December 5, 2012

It's been a pretty busy few weeks. We traveled to Nebraska where husband gave a talk at the University of Nebraksa-Lincoln, and I talked at UNL and Creighton. It was a great trip, and I was very impressed with both schools. I was surprised by how different the schools looked to me now (as a postdoc, and perhaps potential career opportunity) versus when I was an undergraduate student.

Then, we got back and started getting back into the research groove, only to find out on Monday that our daycare is closing at the end of the month, so we have two weeks (because daycares close for the end of the year) to find a new daycare for January.

There is lots of good news, too!

- The last paper from my thesis was accepted for publication (write-up coming soon).

- A manuscript from research done during my postdoc (selection on the Y chromosome) is out for review.

- I received a totally new dataset (RNAseq from humans with Rheumatoid Arthritis) to analyze, and have been learning how to interact with the newest computational cluster on campus, as well as run new software. So exciting!!

- Another postdoc and I are working on some cool ideas for a new project together looking at convergent evolution.

- I'm very positive that a manuscript studying the evolution of strata on the sex chromosomes will be ready to submit by the end of the month.

Wednesday, November 21, 2012

A friend shared this story today, and I was very moved by it. It was a wonderful reminder of the power of acceptance. Although the story centers around the person receiving acceptance, for who she is, for me, the take-home message is about the significance of being accepting of others. Specifically, this line drove that home:

"Her love had given me the final affirmation to move forward and become the person I was always meant to be."

Thank you to everyone who has supported me, and continue to support me. You have helped me become the person I was meant to be. I will do my best to pay it forward.

Monday, November 19, 2012

I think scientists should spend more time making easy-to-understand science snippets, like this:

Maybe not with dogs. Little brown dog would never behave this well. But, something similar. Getting real concepts across in a simple, clear, concise way is not always easy, but it what we, as scientists, have to do.

Sunday, November 18, 2012

I've been doing a lot of writing and editing lately, and yesterday Microsoft Word quit. When I tried to reopen it, I received a strange error message. It seemed so strange that I was compelled to share it here:

Monday, November 12, 2012

This was my year attending the annual meeting of the American Society of Human Genetics (ASHG). Wow! The meeting was enormous, but well-organized. The process for uploading presentations, as well as the technology personnel themselves were fantastic, from a speaker/moderator view. Even though the broad focus is human genetics, I found that, similar to the annual meetings of Evolution or SMBE, the topics vary significantly, and often sessions of similar interest (to me at least) were scheduled concurrently. The venue and schedule were very amenable to switching between sessions, and for facilitating interactions during the breaks. I especially liked that there was space to allow posters to stay up multiple days, and to stagger presenters from each poster topic.

I tweeted less than usual, but I blame this on a conference being too close to home (such that I could attend the conference, but still had all the responsibilities of being "home").

Here's a synopsis of ASHG2012. In particular, I'd like to point out that the Nielsen lab got a bullet point, as did my talk!

"- The Nielsen Group is still working on high altitude adaptations. They don’t see hard sweeps. Of course I didn’t get confirmation of whether these were old variants, but it looks as if a lot of preliminary stuff did not have the power to detect anything in the first group. As usual they are up to something.- Speaking of the Nielsen Group, Melissa Wilson Sayres’s work on purifying selection on Y chromosomal lineages was persuasive to me. Basically, effective population differences (e.g, polygyny) just can not explain the lower diversity of the Y lineages (they ran simulations). Luckily for the phylogeographers this won’t impact the utility of Y trees (positive selection would, but that’s not what she’s talking about). I’m a little confused whether it was Sayres’ talk or not, but these results may explain the discordance in coalescence between mtDNA and Y lineages (the former has a deeper coalescence)."

I didn't mention it specifically, but yes, I do think that purifying selection may be able to explain the differing estimates of the TMRCA (time to most recent common ancestor) obtained from mtDNA and chromosome Y studies, by reducing the time to coalescence for the Y lineage. I'd love to hear what you all took away from the conference.

Friday, November 2, 2012

It was a rough week in the lab. I got a little turned-around on nearly all of my projects at the same time. I generally like having multiple projects, because if one isn't working, there's something else to go to for a break/inspiration/motivation. Not so much this week. With some luck (read: debugging) it ended well, and I'm excited to get started on some new analyses.

Thursday, November 1, 2012

Many great times were had watching Backstreet Law/Till December. This song came up on my shuffle today, and reminded me what a fantastic time I had with good friends, and my future husband, watching this band.

Monday, October 29, 2012

I've been really excited to get started on several different projects. The great thing about having different projects is that there is always something to work on, and leaves me without an excuse about boredom (because I can just switch projects). The bad thing about having so many projects (and not having a lab of my own yet) is that sometimes everything needs your attention at the same time. In a way, being a scientist is like being part of a family. Some projects are constantly begging for attention, others sit quietly and wait for you to play with them. And then, sometimes one project slipped while running around the corner to avoid naptime and needs you to tend its bumped head, while the other project is nudging your arm while whining to be let out to pee, and yet another just wants you to come say hello because you've both been working long days and it seems like you never just enjoy each other's company anymore.

Uh, projects... right.

So, I'm in the position of having a few projects that I'm very excited about, and wondering when I'm going to find the time to complete them all. One step at a time, I guess. That's what keeps me on track. I make small manageable goals, and eventually they'll all get done.

Last night I finished some data parsing and sent it off to my collaborator in Denmark. It is for a project where we're assessing the amount of allele-specific expression in the genome. All autosomal genes have two copies, and generally scientists think that each copy gets expressed at the same level (50% from copy 1 and 50% from copy 2), but there is evidence that sometimes one copy, or allele, is expressed much higher (or lower) than the other copy. This is what we call allele-specific expression (ASE), and together we are working to assess ASE, while accounting for technical variance in the data.

I'm also working on some re-analysis for a manuscript studying diversity on the non-sex chromosomes (autosomes), and the sex chromosomes (X and Y). Our paper was rejected after nearly 11 weeks in review, but I think we have a good chance of acceptance after making some small additions. I'll also be giving a talk about this work at the upcoming ASHG meeting, and am working on putting my talk together.

A third project I'm working on is analyzing evolutionary strata across the whole X chromosome in mammals, starting with humans. I am collaborating with people in Texas on this project, and was fortunate to meet with them in person a little over a week ago. It is sometimes easier to stay focused, when you know your collaborator (or PI, or student) might stop by at any given moment, but, for now, I'm staying on track.

I'm also looking forward to doings some raw RNAseq analysis in humans, studying pig genomes, and looking at expression variation within and between bird species.

Sunday, October 28, 2012

I'm lucky to have only a few stories to share, yet. But, here is a recent example:

While talking with the male driver and male passenger in the Super Shuttle on the way to the airport last weekend, I was explaining my research on sex chromosome evolution. I had just started describing the phenomenon of male mutation bias, where, because most mutations are due to errors during replication, we expect more point mutations to accumulate in the male germline (because sperm continue to replicate throughout a male's lifetime) than in the female germline (because eggs are all formed by a female's birth. The male passenger piped up, "Well, it's a good thing you're a female studying this. I don't think a male could get away with it."

Uh...

I debated pointing out that the first person to introduce this hypothesis was Prof. Takashi Miyata, a male, but decided to let it slide. We all choose our battles, and this one wasn't worth my time. I was more excited to actually share some cutting edge science with these guys, who were asking lots of questions, than get hung up on some perception about who can study what in Science.

I wish I had more opportunities to just shoot the breeze about the cool stuff I'm studying. As a result of bringing up what I do, I learned that the other passenger is the lead administrator for the local children's hospital transportation unit (moving sick kids to the best hospital for their care), and the driver's daughter went to grad school for forensic science. Rock on!

Tuesday, October 23, 2012

This morning the Bear and I got up to get some milk (for her) and make some tea (for me), and she decided she didn't want the milk, but just to sit with me and read books. So we did. Then we got dressed, and I checked my email, while Husband made us some bagels.

After over 10 weeks in review at Nature, my first post-thesis manuscript was rejected. Sigh. I skimmed the reviewer comments and sent them to my collaborators. I was starting to think of how to respond...

...and then the Bear offered me a piece of her bagel and started dancing in her chair.

Sunday, October 21, 2012

Last weekend the Bear and I met up with friends at the Little Farm at Tilden Park. Unfortunately she vomited all over herself and her carseat when we pulled up to park. I think it was a combination of the windy-drive with coughing due to her cold that just affected her gag reflex. Afterwards she felt fine. When I parked to clean her up I told her we were just going home, and she said, "no, farm!". She seemed fine, so I scrounged around (of course I didn't have an extra outfit with me), and fashioned her a dress out of my tank top, pulled up her long socks, and snuggled her up in my jacket, topped off with a hat.

We had a great time feeding lettuce to the cows, geese, goats, and sheep. Then, along with our friends and their 10 month old daughter, we explored the Nature center. Later we met up with some other parents and their kids for a delicious picnic.

When we got home I cleaned out her carseat, taking it completely apart. I was surprised at how far apart I could dismantle it. I hung the cover up to dry in the bathroom.

The Bear had fallen asleep on the way home, but woke up after 45 min, a little disoriented. I picked her up and she fell asleep, so we took a nap together on the couch. It was awesome.

In the afternoon, Husband, Bear and I walked down to check out Sunday Streets Berkeley. It was pretty neat to walk down Shattuck, one of the main throughways here in Berkeley. We only made it near the tail-end of the event, so I can't make an overall judgement of it, other than it was very pleasant to walk around with so many other families, people, and dogs out just enjoying the day. I hope they do it again.

Oh, and, I got into an argument with a woman at the Sunday Streets who was blindly encouraging people to "Vote Yes on 37", the GMO-labelling proposition on the ballot here in California. If she weren't so pushy, I would have been able to avoid her. But... she was spewing absolute nonsense and I couldn't resist telling her so. "Did you know that over 150,000 farmers have committed suicide because of Monsanto?", she said. Ignoring the fact that this claim seems intentionally provocative and perhaps unfounded (although I found the reference here from an Indian filmaker, and have yet to determine its truth), I told her that I agreed that Monsanto is a conglomerate who has done many deplorable things, and I think they should be regulated. But prop 37 doesn't address Monsanto or their actions in the slightest.

This caused her to pause for a minute before she said, "Well, we just want to know what we are eating." I responded that the labeling requirements in 37 are also not sufficient to label GMOs, and appears to be aimed at fear-mongering the public rather than informing them about any potential dangers. It would be, I argued, similar to labeling only red fruits as "containing DNA". I think the general public is not aware that everything we eat contains DNA. And even if they are aware, it would be suspect to label only some fruits as containing DNA, and many people would be afraid to consume red fruits simply because of the label.

Further, the proposition includes many exceptions, including foods that are "unintentionally produced with genetically engineered material". If the goal of the proposition is really to inform the public, then why make exceptions for foods that contain genetically engineered material, just because it wasn't intentionally put there. That's like only requiring labeling of peanut-containing food if the product intentionally contains peanuts, ignoring other products made on the same assembly-line.

There are several other exceptions that make me think this proposition would only increase bureaucracy and tax-payer expenses, while not actually addressing the ethical, social, environmental, or health concerns related to genetically modified organisms. The latter I can get on board with. But please don't try to scare me into legislation with faulty arguments.

Saturday, October 20, 2012

* I sent this letter to the Onward State blog editorial contact today.
Dear Onward State,

As a Penn State alumna, and someone concerned with the image of Penn State and its students, I implore you to please remove Ms. Maggie McGlinchy's access to post on the Onward State Blog.

The mission of Onward State, in its own words, is:

Onward State is an independent, alternative Penn State blog that seeks to foster the student voice through the combination of commentary that is fair, authentic, and sometimes humorous; analysis that is critical and irreverent; and news that is relevant and accurate. Onward State works to generate honest and frank conversation in the hopes of enriching the Penn State community and experience.

Unfortunately, Ms. McGlinchy has repeatedly shown that she is neither fair, authentic, nor humorous. She continues to demonstrate her inability to think critically, or to provide accurate information.

I appreciate irreverence, and encourage frank discussions, but Ms. McGlinchy fails to grasp the subtle difference between irreverence and bigotry. In her most recent failure, Ms. McGlinchy offended countless current students and alumni, with over 126 negative comments accumulated less than two days after publication (here). It has taken just a few moments to assemble some samples of Ms. McGlinchy's dim wit, with numerous more examples of her failure to fulfill the mission of Onward State readily accessible:

Humorous:

(describing "obscure" clubs at Penn State)

"Association of Women in Computing – At first you think “WOOF” then you think $$$$."

(referring to a comment from a student returning from study abroad and her response) “It’s so weird not being able to just order a beer right now.” Guess what, it was weird for me too when I lost my fake but you don’t hear me crying about it. Besides you’re a lot closer to 21 than I am so shut the hell up and black out with me already.

"First of all, as a self-proclaimed University Park elitist, I’m going to tell you this now: Commonwealth Branch campus kids are weird. Not only do they think they’re on the same playing field as you even though they went to Altoona (which, HELLO, is basically a glorified high school and now they’re gonna get a job just as good/better than yours) but they’ll be older and probably offer to buy you beer and tell you to take the bus to Vairo Boulevard or wherever the fuck they live."

"Thinking about wasting $50 on that bandage skirt you saw at Urban the other day? Think again, because when you walk into that frat party you’re going to on Friday you’re going to see it on about 7 other girls– and chances are it’s going to get doused in beer, anyway. Ah, the beauty of going to school in bumblefuck, PA. I mean. can you imagine if I showed up somewhere in shoulder pads or boyfriend jeans? Not only would I go home alone, but probably in a straight jacket as well."

By continuing to allow her to post unchecked on your blog, you choose to disregard the mission of your organization, and to misrepresent the general quality of students at Penn State.

Please consider removing Ms. McGlinchy's access to this broad platform for sharing her insipid idiocy. She will still be free to share her insights on her private blog, but without the implied support of the Penn State students of Onward State. If nothing else, I can only hope that she will take the time to reflect on the long-term implications of her words, on both her own career, and the reputation of Onward State.

Thursday, October 18, 2012

I'm on my way to Denton, Texas to meet with collaborators and give a talk at the University of North Texas. My first meeting is at 8am.

So, I put in a full day today in lab, met Husband and Bear at the park, tried a new (to us) Mexican restaurant for dinner, then came home to pack up, play, shower and read bedtime stories. I hugged Husband and said goodnight to the Bear as he took her back to bed before gathering my things and walking to the BART. I had to make a quick detour to lab to grab my adaptor, in case there isn't a computer for me to use, and I need to plug in my own.

I am very excited to be going. I am also sad to miss anything at home. But, I'm lucky to know that the Bear is in good hands, and I will get to see everyone soon.

---------
Update:
I took the wrong BART train transfer and went North one stop. I realized as soon as I stepped on the train, but it was too late. Still, not so bad because the next SFO bound train was only 10 min out, and there were plenty of seats.

I made it to the airport, yay! Then the voice came over the loud speaker to tell us the AirTran, to zip between terminals is down. Eh, I don't mind the walk.

Getting ready to go through security. Just need to grab my driver's license. Oh. No. Where is it?! I called husband frantic about it. He found it, among the other cards the Bear was playing with yesterday. But, we both realize that there isn't enough time for him to make it here and me to make my flight.

It turns out you can go through security without a government issued ID, if you have two other forms of identification, and you submit yourself and a of your things to a thorough search. The head of TSA here at SFO was actually really great about it.

And, thanks to the iPhone, I have already cancelled my rental car and booked a taxi for the morning. I just need to figure out tomorrow afternoon, but that will come tomorrow.

Whew! Now time to practice my talk and maybe read some papers about the X chromosome.

Tuesday, October 16, 2012

In case you're not on Facebook, I'll start out by telling you that there is a page called, "I Fucking Love Science" that posts many popular science posts. Many of these are mildly inaccurate, or not really even Science, but they're about liking Science.

I understand this person's frustration, especially with the bad science that is being propagated, but, I still think that getting people to like science, even superficially, is a step in the right direction.

However, the association of sexy super-models with being nerdy is something I can agree is ridiculous. I'm all about nerds being sexy, but because they're smart. Smart should be sexy. It is sexy. But nerds are generally awkward, and too busy staying up late reading manuscripts, debugging code, running experiments, and figuring out how things work to spend time waxing, pruning, preening, and counting calories. Sure, most of us aren't completely oblivious, and we want to be healthy, and we want to look good. But I think a sign of a true nerd is that when it comes down to a choice between science or image, science wins.

Monday, October 15, 2012

This morning the Bear and I were on our own. We got ready and made sure to put on our jackets, because it was chilly this morning. The Bear snuggled into her new sweater from Nana, and was surprisingly cooperative getting into the stroller for our walk to daycare. She was a little hesitant to leave me, but then gave Gloria a big hug, and went on it. I grabbed my bag and zipped my coat up and started walking into work.

About halfway to work I passed one of the grates that blows warm air. There was a 50-something looking man, curled up, asleep on the grate. He had no jacket, and no visible belongings. His face was thin, but relaxed in sleep.

This shouldn't happen. No person should be without food, shelter, medical care or clothing.

Homelessness is a problem. It's a problem that stares me in the face every day here in Berkeley.

I am especially impressed with the women's daytime drop-in shelter, which offers breakfast and lunch, a series of programs and counseling to aid single parents in transitioning to long-term housing, and encourages patrons to volunteer to assist with the upkeep of the shelter.

We give food directly to some of the homeless people we've met, and for one particular gentleman, we've given him money directly. But, I am generally cautious about giving money to anyone. Perhaps I'm too cynical, but I really want the money we spend to go towards providing food, shelter, medical attention or clothing. As such, tonight I donated to the women's daytime drop-in shelter.

But, regardless of my desire to give them money, I try to make eye contact, and say "hello", or otherwise acknowledge the people who ask for money along Berkeley's streets. It is the same as I do with just about anyone I pass. Granted, as the cities I live in get bigger and bigger, I tend to stick out more, but I just can't get over my mid-west up-bringing.

I think all human beings deserve to be acknowledged. And, I'm ashamed of how I've changed here in Berkeley. I admit that I don't always interact with people on the streets, especially when I'm alone with the Bear. I can't risk her safety. There's only been twice that I've been genuinely concerned about our safety here.

The first was when we first moved here. The Bear was only 6 months old, and she and I were walking to the grocery store. A woman, who was yelling profanity and fragmented thoughts, was sitting on a bench. As we walked past she stopped yelling and started whispering. When I got about 10 feet away she sprung up and ran to catch up with us. She just stared at the Bear, whispering, and keeping pace with me. I was on a main road, and turned into the first store I came to. She waited outside for us for several minutes, then walked off somewhere else.

The second was a few weeks ago. The Bear and I were walking home from daycare with Little Brown Dog, and a tall man was stumbling up the other side of the street. He saw us and crossed, without looking. He asked if my dog would bite. I said, probably not, but that he is shy (at this point all the hair was standing up on Little Brown Dog's back, and his ears were flat against his head). I started to walk away, and the man blew marijuana smoke at me and the Bear, then started to curse at me for something I couldn't understand. He walked to the middle of the street and yelled at us until I was too far away to hear him.

Poverty is one of the biggest factors affecting homelessness, but these two experiences highlight, for me, how important assessing and treating mental health are for tackling homelessness.

Saturday, October 13, 2012

I was pretty impressed with the thoroughness of the website, isidewith.com, for their coverage of many different issues that are often important to voters in the US.

I was surprised to see that I am nearly evenly split between agreement with Barack Obama and Jill Stein. I still haven't decided how I'm going to vote, though.

In the two-party system we seem to support here in the US, I feel like choosing someone other than Obama or Romney is basically throwing my vote away. However, perhaps it is because everyone feels like this that the two-party system persists. I'm sure it is a little more complicated than that (e.g. funding behind the two major party candidates, voters having the time to investigate all candidates, candidates being able to get on the ballots in every state, etc...).

The website, above, however, was very useful, in my opinion, for giving me a starting point to learn about the ways the candidates differ on a variety of topics. I would like to take this quiz a few times to see how consistent my results are, but I'm not sure I'll be that motivated. I did take it twice. The first time, I agreed with Jill Stein on something just above 90%, and she was my top hit, but then I accidentally closed the browser. The image from above was taken from the summary of results a few days later.

But, rather than test out their quiz, I think I'll spend the time reading up on all the propositions here in California. We got our mail-in ballots yesterday (yay!), and they need to be returned as soon as possible.

My K99/R00 was submitted this morning. The revisions for the last manuscript from my thesis were submitted yesterday. I got mini-scooped on an idea, but it is exciting because it shows that the idea was actually valid - and was published in Genome Research. I'm reading up on background for a new and exciting collaboration.

Wednesday, October 10, 2012

I am very new to the whole grant submission process, but can already say that there is some tension between the Sponsored Programs Office (the people who submit the grant on behalf of the individual and the University), and the individual PIs. There are deadlines, and things get stressful for everyone all at the same time.

I would like to pause and thank the SPO contact, and SPO office here at Berkeley, for helping me get my K99/R00 in order. Between the two, they found a few small errors that would have added up to a big "doh!", when I realized what I'd done:

2. Added an older version of my mentor's statement with placeholder comments (opps!).

3. Calculated the overhead including the fringe benefits, when they should have been excluded. This one is, in my opinion, much more minor to the acceptance of the application, but still good to catch.

4. Not errors, so much as tidying up the way I presented the budget (I had too much detail that might have painted me into a corner if things change between now and the possible funding date).

Those four items took me the better part of the night to complete but I think hope everything is ready to go now.

In other news, the revisions of the last manuscript from my thesis work should also be submitted by Friday (or else we pass a deadline, and it will be considered a new submission). This will be the fourth time out to review, so let's hope we addressed everything properly. I really think we did. This is another case, actually, where I should send out acknowledgments and thanks. The comments from the reviewers really helped make the manuscript much better. So, thank you anonymous reviewers.

Tuesday, October 9, 2012

We don't have cable, so miss a lot of commercials. Usually that's a good thing, but thanks to the internet, I can watch commercials whenever I want (yay?).

I came across this commercial for Luvs, and wanted to thank them for featuring a breastfeeding mom. I completely felt like the first time mom when we started. I was more comfortable after a few months, but still felt awkward, even when it was just needing to pump at a Scientific conference. We'll see how I do whenever we get around to #2:

Monday, October 8, 2012

I've been reading up on the plethora of ballot initiatives here in California, and was excited when our voter book came in the mail today. I turned it over to find out polling place and instead read this:

What the what?! It seems supremely strange to me to have no polling place, but the National polling place database and the local Alameda County polling place both have our address listed as without a polling place. Weird.

I guess I'll just have to get my vote out in the mail early this year. It will feel a little anticlimactic.

Plus, how am I supposed to show off my awesome citizenship without my "I voted" sticker?

Friday, October 5, 2012

PBS was targeted as one of the first things the Republican candidate would cut to reduce federal spending. The silliness of highlighting cutting PBS funding as a method for reducing spending is stated, very nerdily, by Dr. Neil DeGrasse Tyson:

But, I don't even know that this is very important. I agree that wasteful spending should be reduced, no matter how small a proportion of the budget it is. But I do not think that PBS is wasteful spending. In addition to supporting educational television, and providing a resource to children whose parents cannot afford or choose not to send them to preschool, PBS is a system of local stations that provide jobs, and connect people within communities.

For more than 40 years, Big Bird has embodied the public broadcasting mission – harnessing the power of media for the good of every citizen, regardless of where they live or their ability to pay. Our system serves as a universally accessible resource for education, history, science, arts and civil discourse.

and,

A key thing to remember is that public television and radio stations are locally owned and community focused and they are experts in working efficiently to make limited resources produce results. In fact, for every $1.00 of federal funding invested, they raise an additional $6.00 on their own – a highly effective public-private partnership.

and,

Numerous studies -- including one requested by Congress earlier this year -- have stated categorically that while the federal investment in public broadcasting is relatively modest, the absence of this critical seed money would cripple the system and bring its services to an end.

Wednesday, October 3, 2012

You know you're a geek when things like this are worth your time to investigate.

I've been doing a lot of writing lately, and was surprised to see a colleague of mine adding two spaces after a period. I had learned the "two-space" rule in elementary school, but was taught during college and grad school to only use one space after a period. But, after discussing it with my friend, I started to question whether I was right. Should I instead be using two spaces? How much does it matter?

Cue the internet.

Instead of going into all the details myself, I'll point you to a few places where other people have gone into detail, and highlight a few parts. Basically, however, typewriters used the same amount of space for each letter (monospaced), and so two spaces following a period made it easier to read, but we have proportional fonts now that make the two spaces unnecessary, and even obstructive.

"Who says two spaces is wrong?" they wanted to know.Typographers, that's who. The people who study and design the typewritten word decided long ago that we should use one space, not two, between sentences.

Because we've all switched to modern fonts, adding two spaces after a period no longer enhances readability, typographers say. It diminishes it.

The use of proportionally spaced type makes double spaces after a period unnecessary (if they ever were). The extra spacing is often distracting and unattractive. It creates 'holes' in the middle of a block of text — trapped white space on a smaller scale.

Although how many spaces you use is ultimately a style choice, using one space is by far the most widely accepted and logical style. The Chicago Manual of Style (1), the AP Stylebook (2), and the Modern Language Association (3) all recommend using one space after a period at the end of a sentence.

So, the take-home message is to use one space following a period. Full stop.

Tuesday, October 2, 2012

The little Bear and I were playing at the park last week. A pair of parents were discussing dogs, and then one turns to me and says, "Hey, you study genetics. So, how closely related are dogs and wolves?"

Being a complete nerd, and failing to recognize the social situation I was in, I started by responding with, "Well, that depends. If you're talking about the ability to mate, or about genetic relatedness, and then whether you're looking at genes or intergenic...".

At this point, the guy who asked me butted it, "Wait, wait, wait. I just wanted to know a number. Give me a number. How similar are dogs and wolves? 90%? 99.9%?".

Oh.

I then tried to explain that I didn't know the exact number, but the father responded that I could just give him a ballpark estimate. But, by this point, he said, he didn't care about it anymore.

Communicating science fail.

Later in the week, the dog-wolf discussion came up again, and I told the father that I didn't want to give him an incorrect answer, and have him lose confidence in my scientific credentials. He assured me that he would never have checked up on it, and simply wanted to know the little factoid.

Therein lies the problem. Once people know that I study evolution, or anything related to genetics, many just want me to spew random factoids. But that isn't how Science works.

Science isn't a bunch of mini-absolutes. It is trends, and correlations, and interpretations. When enough of these are independently confirmed, then we have confidence in the results.

I don't know how to convey this to the public in a short response. I don't want to become a factoid-box. I don't want to proclaim myself an expert in fields where I'm not. I don't want to perpetuate the stereotype that scientists think we are always right. But, at the same time, I want to convey the confidence that can be concluded from hundred, or thousands, of independent observations.

So, do I know exactly how closely dogs and wolves are? No, not off the top of my head. But, I do know that modern dogs and modern wolves share a common evolutionary ancestor, and, after a quick literature search, it was likely about 130,000 years ago.

What to do? Perhaps have qualified answers ready. Something like, "I don't study {dogs} specifically, but {dogs and wolves} are {more} closely related than humans and chimps, so probably about {99%}."

Genomics may be a tool of interest to Native American communities. However, Native Americans are underrepresented in occupations and careers incorporating genomics and the sciences in general. According to estimates from the Census Bureau, Native Americans hold at least 5x fewer occupations involving science and engineering relative to their total population in the United States. Furthermore, there is a lack of Native Americans in advisory roles to the scientific community, which prevents proper relay of cultural values and concerns that developed as a result of difficult histories of Native American encounters with science. This lack of leadership also leaves few individuals who can explain the uses and limitations of scientific research to Native American communities that are considering participating in a scientific project. To address this problem, faculty and students at the University of Illinois Urbana-Champaign campus are working with leaders in scientific and Native American communities to create the Summer Internship for Native Americans in Genomics (SING) Workshop.

There are 47 percent of the people who will vote for the president no matter what. All right, there are 47 percent who are with him, who are dependent upon government, who believe that they are victims, who believe the government has a responsibility to care for them, who believe that they are entitled to health care, to food, to housing, to you-name-it -- that that's an entitlement.

I agree, it is an entitlement. It is an entitlement that every prisoner has, and was even a regulation at Alcatraz Prison (I'm not sure what the regulations are at modern prisons, but I image they are the same). I think all Americans, heck, all people, should be entitled to food, clothing, shelter and medical attention.

To be fair, I don't think Romney is heartless. And, I truly don't believe he intended to imply that people don't deserve these basic needs, but he does provide some good blog fodder.

Wednesday, September 26, 2012

I'll give away the punchline now. This is about poop. If you don't want to read any further, please stop now. Seriously, poop. Poop. And not the science of poop, or, "hey, here's this neat thing about poop", but, an "I am a parent, and here is one of the bizarre things that happened to me, and it involved poop. You might not want to hear about it, but this is a blog, so you don't have to continue reading, and I'm going to write it because parents need to commiserate, so here it is: poop" kind of story.

I'm in the final stages of applying for the NIH K99/R00 Pathway to Independence Award. I can blog more about this process if there is interest. For now, I wanted to write about how it has gotten me thinking about the skills necessary for transitioning successfully from a postdoc to an independent researcher.

Coincidentally a friend shared this resource from the National Institute of General Medical Sciences (NIGMS). It is a series of video-presentations from a workshop held on the NIH campus in March 2010. The topics are quite diverse, but the ones that jumped out at me are:

I didn't have time to post this last night because I was actually working, so here it is now.

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I'm nearly finished with my NIH K99/R00 application. Whether I am or not, the deadline is to get it to my Sponsored Programs Office by Monday Oct 8. After receiving abundantly helpful comments from my colleagues and mentor, I really got in the groove this afternoon putting the finishing touches on the research proposal.

And... then I realized I had 15 minutes to make it to daycare. Usually I leave myself 25 minutes to get home and let Little Brown Dog out, then hike up to pick up the Bear. Today, because of a great "science" groove, I got out of my "mommy" groove. Yes, I consider myself "mommy" to both my daughter and my dog. I realized I didn't have time to get home, so I decided to go to daycare first then come home and let out Little Brown Dog. Poor Little Brown Dog.

I raced down the stairs, and about halfway through campus I realized I left the milk in the fridge at work (we were almost out of milk, so, in an effort to be efficient I picked some up on my way to work, doubling with another errand). Sigh.

At daycare the Bear was not unhappy, but not her bubbly-self. Until I tried to put her in the stroller. Then she was definitely unhappy. She voiced her displeasure at being forced to sit the entire trip home.

Once home, the Bear was very happy to see Little Brown Dog. We all went out for a walk. Little Brown Dog was relieved. The Bear happily played outside, and all was well in the world.

We came back inside and the Bear helped me eat bananas make some Banana Bread:

Don't worry, we had plenty of bananas, and she did help with lots of stirring after each ingredient addition. I accidentally mis-measured (I grabbed a 1/3 cup instead of a 1/2 cup without realizing it), so the bread isn't as sweet, but is still pretty tasty.

The Bear colored the counter on some paper while I made French Onion Soup. It was delicious with toasted rolls and melty cheese. We both ate our fill, then while I did dishes, the Bear decided to paint her head with the leftover cooked onions in her bowl. It wasn't pretty. I'm a little embarrassed to share this picture, but she was playing so quietly and contently that I just let her do it so I could finish the dishes and take the banana bread out of the oven without worrying about her getting hurt.

Oh. my. goodness:

Banana bread done. Dinner finished and cleaned up. Now it was definitely time for a bath. Afterwards the Bear and I enjoyed some quiet time sitting together on the couch, she with her warm milk and me with some hot tea. It was... very nice.

We sang some songs, told stories, and made funny faces. Then, just after 8, Scott came home. (Seriously, 5:30pm, 5:45pm by the time everyone shows up, is a terrible time to have routine lab meetings. End rant.) We brushed teeth (yay!), went potty (yay!) and she fell asleep very easily (yay!).

So, all-in-all, a pretty good night. I guess the grooves weren't so mis-aligned.

Now, we have a few hours to get some work done. I see python code in TextWrangler, and some sort of molecular orbitals on Scott's laptop. I'll be focusing on the K99, of course. :)

Friday, September 21, 2012

Another meme going around is "International Book Week". I couldn't find a reference to this, but I did find, "Banned Books Week", which is held the last week of September. I remember our elementary and high school libraries celebrating this, and think it is probably the origin of the "International Book Week" trend.

Still, I thought it would be fun to participate. The game I saw this morning said:

It's international book week, grab the book closest to you, turn to pg 98 and put the 2nd sentence as your status. Don't mention the book title.

So, here goes!

First closest book:

"Genital presentation is probably an adjunct to olfactory communication in such cases and this might represent one of the evolutionary origins of presentation behaviour among the diurnal anthropoids."

Wednesday, September 19, 2012

I hit some magic stride, stayed up crazy-late last night (which is only crazy late because I had no option to sleep in this morning) and finished the first draft of my research proposal. Yay! There is still a lot of work to do, but for me, getting the first draft written down is much harder than editing.

Last night and today I also found time to work on manuscript revisions, which are due the same time as the grant, and to analyze data quality for a project of mutual interest with a new labmate. And then about 4pm rolled around... and it all caught up with me.

Luckily it was near time to leave to pick up the Bear from daycare. We skipped the park today, and instead came home, painted, played monster trucks, babies, then took a bath and had dinner. Now, we're going to cuddle up and watch Despicable me. I'm hoping I don't fall asleep before she does.

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Update: We ended up only watching the last half hour, then dancing, of course, to the boogie music. Chip was whining, so we all took a walk around the block, then the Bear "helped" me with dishes, brushed our teeth, Bear peed on the potty (yay!), and we read a few books (I read the last one twice, then she "read" it back to me).

Then, bedtime attempt #1: fail.

Tried the potty - nope. I made some hot tea for me, and warm milk for the Bear. We just sat in silence enjoying our drinks, then back to bed. A little rocky, but she fell asleep just after 9pm.

I'm getting up early to drive with some labmates for a lab retreat, so I'm going to get to bed... after I work on some of the supplementary grant items.

Thursday, September 13, 2012

I'll be focusing on fellowship-writing for the next two weeks, so if you see me posting regularly here, please lay on the guilt until I get back to writing/proof-reading/editing, or can provide you a copy of the finalized application.

"And, in contrast to other research, gender differences among graduate students and postdoctoral fellows disappear. Family factors impede talented young scientists of both sexes from persisting to research positions in academic science. In an era when the global competitiveness of US science is at risk, it is concerning that a significant proportion of men and women trained in the select few spots available at top US research universities are considering leaving science and that such desires to leave are related to the impact of the science career on family life."

I assume that their definitions of male/female are based solely on self-reporting (and didn't offer a transgender category), so I will use the same terminology here. Here are the take-home messages:

1. Faculty with children work fewer hours than those without, but the difference is much lower than stereotypes would suggest:

Hours of work
No children With childrenWomen/MenWomen/Men 59.1/57.854.5/53.9

2. Women faculty have fewer children than men (although the average for both is under 2), and are twice as likely to report that they had fewer children than they wanted.

3. Even though women have fewer children than men, women are "more satisfied with their lives than men", suggesting, "that having fewer children than wanted has a more pronounced effect on life satisfaction of male scientists."

My conclusion: making the academic atmosphere more family-friendly will be beneficial to all who work there, without adversely affecting productivity.

Saturday, September 8, 2012

Okay, so I've been thinking a lot about the arguments for home-schooling and the arguments for organized-schooling, and I think that there is no benefit of home-schooling that cannot be accomplished by a parent, whether their child is in school or at home.

There is one huge, glaring difference, that will prevent me from home-schooling my daughter.

I've been struggling with exactly how to describe it, but I guess it can be boiled down to a word: Diversity.

No matter how many course materials I put together, or how many field trips I take her on, or how many sports and outside activities I enroll her in, I will always be the one teaching her. What if she doesn't learn the way that I teach?

Part of what can make school boring (aside from the subject material), is the teacher. For argument's sake, let's say I'm an effective teacher. How do I know that I am an effective teacher for my daughter's learning style? Secondly, if I am an effective teacher for her, what's to say that integrating other methods would not also be useful. There is visual learning, oral learning, kinesthetic learning, and then there are as many ways to present information as there are people. Diversity.

There is a huge benefit in learning how to learn. And, learning how to learn in different ways.

This causes our brain to switch modes, to think outside of the box.

Perhaps there isn't enough of this in organized schools, especially schools that feel constrained by standardized theists. And we should work to change this.

Contrary to the propaganda of some home-school advocates, not all teachers have the same opinions. Shocker. Y'know who does have generally consistent and fairly standard opinions. Each one of us. As individuals, we are biased in what we present and how we present it. Even the most open-minded person has opinions, and keeping these opinions out of all teaching is close to impossible. And, in many cases, being exposed to a diversity of opinions, relevant to the topic, can enhance education.

By allowing my child to learn from different people, especially those people whom I may disagree with, I am helping her learn how to think critically, to assess information. Of course, this does require that I, as a parent, actually engage with my child outside of school. I need to listen to what she is learning. I need to have her show me and tell me and teach me what she is learning. In this way I can not only reinforce her "learning to learn", I help her to "learn by teaching". I can also assess whether her teacher is one of the many excellent educators in our country, or one of the few that need to find a different career. If it is the latter, I can, as an involved parent, take actions to facilitate said career change, or at least ensure my child is not subjected to that individual's idiocy.

Choosing to home-school is, in my opinion, the worst form of helicopter parenting. Assuming that no one could possibly teach your child everysinglesubject better than you is not only arrogant, it is foolish, and patently untrue.

Friday, September 7, 2012

Teachers should be paid more. It's a proven fact that the childhood experience at school usually determines whether or not a person is going to go on to college. Professors have it easy and get paid too much for not caring whether a student passes or not. It's true, they get paid more that [sic] school teachers and they don't really do half the job that school teachers do. It's not they're [sic] responsibility to hold the college student's hand and make sure they pass, they're another pay check usually.

The writer is being as dismissive of professors as many people are of school teachers.

In fact, University professors are being expected to hand-hold, more and more. They also, generally, must design course materials to effectively convey information to much larger class sizes and meet with students regularly. At the kinds of Universities I will be applying to, you must be an excellent teacher - making sure students are engaged and learning, while also participating in professional service and committee work, conducting top notch research, applying for grants and fellowships for your own graduate students and postdocs, in addition to mentoring undergraduate students (not in your courses) who also expect you to hold their hand. Professors still receive phone calls and emails from parents upset about grades, while, unlike elementary/high school, the students have the freedom to skip every class, and expect to still earn a 4.0 for their pre-med major. It doesn't help anyone to perpetuate misconceptions about how much effort some educators put in versus others.

Yes school teachers are underpaid, but I think many people over-estimate the salary for the average university professor.

EarningsDuring the 2005-2006 school year, elementary, middle, and high school teachers with a Bachelor's Degree who were just starting out in their career earned an average of $33,227 a year. In May of 2008, the median salary for all teachers in this education level was between $47,100 and $51,180. For the lowest ten percent of these teachers, the average was between $30,970 and $34,280 a year. For the top ten percent, the average was between $75,190 and $80,970 a year. Some ways that a teacher can increase their annual salary is to coach sports, monitor extracurricular activities, teach summer school, perform other job duties for the school over the summer, obtain a national certification, or become a mentor teacher.

For college and university professors, the salary that a professor will earn depends on which college they work for, the rank of the college, the field of study they teach, and the number of years they have worked for that college. In May of 2008, the median salary for all college teaching positions was $58,830. For the middle fifty perfect of the teachers, their salary ranged from $41,600 to $83,960. For the lowest ten percent of all teachers, their salary was under $28,870. For the highest ten percent of all university professors, their salary was over $121,850. Some ways that a professor can earn more money than their salary is by teaching extra courses, doing research projects, publishing books, and other things. They also receive special benefits such as free tuition for themselves and family members, free access to university facilities and equipment, and paid leave.

Or, if you'd rather talk about comparing the highest paid professors versus highest paid high school teachers, see this reference, showing how they are astoundingly similar.

I completely agree that school teachers are undervalued and underpaid, but so are many post-secondary educators!

It's frustrating that fellow educators think that my (soon-to-be, hopefully) job is half the work of a school teacher. The job is different. The stresses and the foci are different. The teaching styles and the grading are different. They are different jobs, with different responsibilities, dealing with students of different maturity levels. Is it harder to deal with kindergardeners, or teens, or young adults? It doesn't really matter.

We are all educators, and being divisive and dismissive is not only unfair, it distracts from the real issue: Educators, all educators, are undervalued.

Thursday, September 6, 2012

theadvocacyof women's rights on the grounds of political, social, and economic equality tomen.

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It is only in the past year or so that I realized I was a feminist. By simply wanting to be treated the same as a man, I am a feminist. By thinking that all genders should be treated with equal respect, I am a feminist. By working for equal parental rights, by advocating against gender discrimination, and by voting for marriage equality, I am a feminist.

And, as a parent, now, I'm worried about my child, my daughter.

Despite not having cable, and not seeking it out, I still hear celebrity gossip. What struck me recently was the emphasis placed on the breakup of Twilight co-stars, specifically the over-the-top derision of Kristen Stewart for her actions, who has now been dubbed a Trampire. From the linked article, the following paragraph was especially frustration (the bold emphasis is mine):

But for young women, theculture of slut shaming that the Kristen Stewart scandal representswon't go away. I might not be concerned for K-Stew, but Iamconcerned for all the young women today who are tuned into this scandal, ones who are learning that it's not okay to screw up, ever. Chris Brown can publicly beat the hell out of his girlfriend but still be played on the radio and win Grammys. However, if you ever cheat on your boyfriend, your life is over and no one will ever want to be associated with you. Almost no one will blame the much-older guy you cheated with, and it might actually make himmore famousand help his career. Few will care that he was your boss and in a position of authority or that he may have have taken advantage of your youth and relative inexperience. Everything is your fault, and your life will be threatened over it. If you are a trampire, you will be publicly staked for it, even though cheater Ashton Kutcher recently emerged relatively unscathed by the media. No one asked for him to be fired fromTwo and a Half Men.

If the underlying culture in America is still to blame, threaten, and slut-shame a woman for infidelity, but expect and accept it from men, then we still have a long way to go.

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